Variant report

Variant	rs12239954
Chromosome Location	chr1:86054697-86054698
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10158408	0.83[AFR][1000 genomes]
rs12072027	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs1329961	0.86[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1576423	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17394091	0.90[AFR][1000 genomes]
rs17398175	0.90[AFR][1000 genomes]
rs34746573	0.90[AFR][1000 genomes]
rs6658857	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6673340	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9651137	0.87[CEU][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9803850	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv3391173	chr1:86005637-86337469	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86048800-86081200	Weak transcription	Gastric	stomach
2	chr1:86049000-86068400	Weak transcription	Psoas Muscle	Psoas
3	chr1:86050600-86054800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr1:86051000-86062800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:86052200-86055000	Weak transcription	Osteobl	bone
6	chr1:86053600-86054800	ZNF genes & repeats	Fetal Intestine Small	intestine
7	chr1:86053600-86055200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:86053800-86055000	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr1:86053800-86064600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr1:86053800-86071400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr1:86054000-86057600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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